After purification via flash chromatography, my ester is in ethyl acetate with 10% acetic acid. Is there any way to remove the acetic acid without destroying the ester?
Have you tried extraction with water? The acetic acid goes into the water leaving your ester in the ethyl acetate. Saturating the water with salt helps keep the ester in the ethyl acetate (look up salting-out effect). I'm assuming the ester isn't water soluble.
If the ester is water soluble, try a flash reverse phase column. Get it into water as described for the extraction, except no salt. Load the aqueous solution onto a C18 column, use a water wash to eliminate the acetic acid followed by a step gradient to wash the ester out in methanol or acetonitrile. For an example of removing a compound from DMSO-D6 (similar problem, high boiling solvent), see: http://www.teledyneisco.com/en-us/liquidChromatography/Chromatography%20Documents/Application%20Notes/Removal%20of%20Non-volatile%20Solvents%20with%20RediSep%20Rf%20Gold%20C18Aq%20Columns%20App%20Note.pdf#search=c18Aq
Thank you for your answer. I have already carried out flash chromatography and fear that a second purification process would greatly reduce my yield. Could the extraction in combination with water and acetic acid not lead to hydrolysis of the ester?
Perhaps a little, but addition of a small amount of base such as ammonia would reduce the reaction. Remember that too much base also hydrolyzes esters. As most of the acetic acid will be in the water, away from your ester, the reaction should be minimal.
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